Chuck vs the New Intersect
by ZebZ
Summary: Picks up immediately after the season finale. What secrets and new features are hidden in the new Intersect? How will Chuck handle the changes? What happens to the team... if there still is a team?
1. Surprises

**Chuck vs The New Intersect**

**Chapter One/Prologue**

Chuck stood perfectly still, staring at his former handlers. "Hey guys, I know kung fu."

His former handlers stared back, not knowing what to say. The stand-off lasted for a few seconds.

"I know kung fu," Chuck repeated slowly. With a very confused tone and measured breath, he continued. "I'm not supposed to kung fu. How do I know kung fu?" Slowly he turned and looked at the first generation Macintosh and the now-dimmed Intersect Cube. "Oh yeah."

Sarah's eyes followed Chuck's gaze and joined him in looking at the machine in the center of the windowless room.

She was momentarily overwhelmed with a mixture of pride and fear, allowing only a brief audible gasp. "You downloaded it again?" she asked as a question, even though she already knew the answer.

Casey grunted, breaking his silence.

Chuck slowly spun around, silently counting the number of motionless bodies on the floor. He stopped when he saw a small crimson pool of blood. "Bryce is dead."

Sarah steeled herself before she responded. "Yes. We know. Did he do this to you? Did he make you put it back in?"

"No. I did this. He was already... he was already shot when I found him. He told me to destroy it. To end it all."

Chuck finally brought himself to look Sarah in the eye. "But I couldn't. It's too important. I knew I could handle it. I had to do this. I wanted to do this."

They all stood silent again for a few seconds before Casey cleared his throat. The other two shifted their attention to him. "Chuck? Can you undo these ties? We need to call in a clean up crew and get Beckman on the phone. And figure out what to do now."

Chuck shifted his wait and began to close the distance between him and the NSA agent. "Oh. Yeah. One sec, lemme just... OW! WHAT THE...!" He crumpled over in pain.

Sarah and Casey were to him instantly and instantly in agent mode. "What's wrong? Talk to me!"

Chuck's eyes rolled back into his head for a brief second before he shook it off. In a somewhat monotone voice, he responded. "I injured myself while taking down the traitor and his team. My Intersect programming assessed the situation and determined the most effective course of action was hand-to-hand combat, but my body's lack of requisite muscle conditioning resulted in multiple muscle tears and strains in virtually all muscle groups and joints. Most severe are tears in the biceps brachii and brachialis near the posterior proximal radioulnar joint, followed by a strain of the semimembranosus muscle and distal semitendinosis tendon, resulting in fluid build-up around the tibial nerve. Additionally, I experienced hyperextension of the anterior glenohumeral joint while attempting rapid lateral rotation. Typical recuperation time is 3 weeks of rest, followed by 2 to 4 weeks of physical therapy. Surgical correction is necessary roughly 37% of the time."

Casey grunted questioningly. "Come again?"

"I, uh, pulled every muscle in body doing my best Stretch Armstrong impression while, um... whatever the hell it was I did back there. I feel more like Bruce Vilanch than Bruce Lee." Chuck's expression slowly changed from confused apprehension to a slight grin. "I sounded pretty smart just now. I mean, I said it. And I didn't make it up. The Intersect diagnosed that and I don't doubt it's the absolute correct prognosis. But, yeah, that was kinda neat how that worked. Absolutely terrifying in some, ok many, ways, but still neat. Oh wow, I probably know as much medical stuff as Ellie and Captain Awesome." He paused for a breath as his was overwhelmed by his own excitement. "I'm not feeling so good."

Casey cocked an eyebrow. "Chuckles. Hey. Yeah, you. Look at me. Undo these damn ties before you hyperventilate and pass out. I'm not going to carry you out of here."

Chuck pushed himself up very slowly and released both Casey and Sarah. The NSA agent was immediately on the phone and pacing back and forth. Twenty minutes later, a crew was on site and leading the enemy agents away and preparing Bryce's body for transport back to Washington.

Sarah and Chuck were standing along one wall, consumed by their own thoughts while watching quietly over the scene in front them when Casey came over. "Let's go. Conference with Beckman in 30."

Twenty minutes later, the trio was at the Orange Orange, preparing to descend into the Castle.

Chuck was gingerly navigating his way down the 23 stairs. "Ouch." Step. "Ouch." Step. "Ouch." Step. "You know, this can't be up to ADA spec. This place has 'OSHA violation' written all over it." Step. "Ouch." Finally at the bottom step, Chuck shuffled to the nearest chair and collapsed into it and dropped his forehead on the desk in front of him with an unceremonious thud. "Ouch," he spoke into the tabletop. "Add concussion to the list."

Sarah sat down next to him and rubbed his back, avoiding his swollen shoulder. She struck a devious expression as she tucked a stray curl behind his ear, leaned in and whispered to him. "Don't worry, when we're done here I'll take you home and give you a nice relaxing sponge bath to sooth those achy bones of yours."

Chuck's head shot up, eyes bulging, cheeks already blushing rosy red. He quickly winced, though. "Ow! Make that concussion and whiplash." He then smiled despite the new pain. "But it'll be worth it."

Across the room Casey muttered to himself.

Seconds later, General Diane Beckman appeared on screen in front of them and immediately began the debriefing, choosing to forgo a greeting and other formalities. "Colonel Casey, Agent Walker. What the hell happened today? I want an explanation and I want it… wait a second. Mister Bartowski, didn't I clearly establish that your involvement is no longer necessary? Why are you present? What is going on here?"

All eyes were on John Casey, who suddenly refused to make eye contact with anybody.

The General was impatient. "Well? I'm waiting. I want to know how the day started with the Intersect cube in our possession and ended with Ted Roark, a room full of Marines, and Agent Larkin all dead and the Intersect cube destroyed. I hope for the sake of your careers you have a damned good explanation for this disaster."

Casey finally spoke up. "General, there is one more bit of information I didn't inform you of on the phone. I wanted to wait until I could be absolutely sure we were secure and there was no chance of anyone intercepting our transmission or even just overhearing me."

Beckman leaned forward, and raised her brows. "Well? Spill it."

"Larkin was killed in action and the Intersect Cube was lost, but the Intersect itself…"

"… is in me."

"It's WHAT!"

Chuck stood up, ignoring the pain in his legs, and repeated himself. "It's in me. Bryce… Agent Larkin was already incapacitated when I found him in the Intersect room. It was evident that he wasn't going to survive his wounds." Chuck gulped, not looking forward to how Beckman was going to react to the next part of the story. "Casey and Sarah were holding off Miles and his crew a few rooms over but I could tell they were outnumbered and outgunned. So rather than let the Intersect fall into enemy hands, I downloaded it into myself and then destroyed the cube."

The General was nonplussed. "Well, Mister Bartowski. Welcome back to the fold. You, of course, realize that you are now property of the United States Government again." She paused to sigh, as if wondering who or what entity she'd pissed off in a past life. "I'm reinstating Operation Bartowski for the time being."

Sarah spoke up, worry evident in her wavering voice. "The time being?"

Beckman folded her hands and focused her attention at Sarah. "Yes, the time being. As I'm sure you recall, I ordered the asset placed in a secure bunker once already. I'm doing it again. Your team, as well as now Castle itself, has become compromised. I've had enough of this. It's time to do what should've been done two years ago."

Sarah stood up, "But you can't!"

She was immediately cut off by the figure on the video screen. "Yes, I can, Agent Walker. And I will. Agent Casey, you will arrange for transport to Wash…"

Nobody noticed Chuck's eyes flutter. "No, he won't. I'm not going into a bunker."

"Excuse me, Mister Bartowski. I am in charge here. You will go. Colonel Casey arrange..."

Chuck stared her down, eyes unwavering. He spoke firmly and deliberately. "No. I am staying. And Sarah and Casey are staying with me."

Everyone was taken aback by Chuck's sudden assertiveness.

"The Intersect has just taken it upon itself to inform me of Scenario Seven. I assume you are familiar with that little exercise, General?"


	2. Revelations

**Chuck vs The New Intersect**

**Chapter Two**

Chuck Bartowski was in a stare-down with General Beckman. "I am staying. And Sarah and Casey are staying with me." The normally pliant nerd had given way to an assured force of will. "The Intersect has just taken it upon itself to inform me of Scenario Seven. I assume you are familiar with that little exercise, General?"

Diane Beckman had always prided herself on maintaining an air of authority and masking any fissures of apprehension. But right now, behind her steely eyes, pursed lips and furrowed brow, she cracked for the briefest of moments. She was suddenly at a disadvantage against a potentially damaging adversary. He knew about Scenario Seven. Shit. This could be very bad if she didn't regain control quickly.

She clasped her hands and leaned forward toward the video monitor. "Mister Bartowski, if you are implying if any way that any awareness of Scenario Seven will keep you out of a secured facility, you are very mistaken. The United States government will not negotiate with extortionists. Anything you do to betray such classified information will be considered treasonous action and will be quickly and severely dealt with, do I make myself perfectly clear?"

Chuck's veneer cracked, and he took a step backwards to steady himself. "What? Wait. Hold on a minute. What? I wasn't implying…" He jerked around to look at Casey and Sarah beside him, who were both visibly just as shocked as he was. "Casey, I wasn't… I wouldn't." "Sarah, I don't… I'm not… I just meant… I couldn't…"

All traces of the Intersect-boosted façade were shattered. Agent Carmichael had clearly reverted into a very confused and frightened, stammering Chuck Bartowski. He gulped in an effort to compose himself, but when he opened his mouth to speak again nothing came out. He was at a complete loss.

John Casey's glare could bore a whole through Chuck's skull. He whispered audibly, "Say something, moron."

Chuck looked up the video screen. Beckman looked back, impatiently, as if restraining herself from pouncing again on the hapless man. He breathed in deeply and closed his eyes for a few seconds. Exhaling slowly, he willed himself to continue.

"General, have you ever watched Star Trek?"

A pregnant pause filled the room as everybody tried to process the last statement.

The General tilted her head slightly to the side. "Have I ever _what_? Mister Bartowski, are you feeling okay? Do you need medical attention?"

Sarah coughed, feebly attempting to mask a partially stifled laugh. Casey hung his head and muttered to himself, "Oh, Jesus."

Chuck ignored the goings-on, "I'm asking honestly, General. Are you familiar with the Star Trek story universe? Specifically, the legendary Starfleet Academy training simulation involving the ship Kobayashi Maru?"

Despite her better instincts, Beckman allowed Chuck leeway. "Go on, Mister Bartowski. This had better be leading somewhere."

"The Kobayashi Maru was a ship in a training simulation used to gauge the character of command-track cadets. It was first shown in on screen as the opening scene in the second movie, _The Wrath Of Khan_. Lieutenant Saavik, played by a young Kirstie Alley, was the one being tested. It was her first feature film and her part was rather forgettable, except that she cried at Spock's funeral even though she was a Vulcan and Vulcan's don't show emotion, but the producers explained that away as her being of both Vulcan and Romulan heritage. I mean Spock was half-human and he managed to keep himself together, but that always seemed to me like a bit of a cop-out that left a sour test in my for the rest of the movie. And then the whole 'Khaaaaaan' thing was just…"

Casey cleared his throat.

"Oh, yeah, right. Sorry. The test was designed to determine how officers-in-training would handle an impossible situation. The simulation goes that the Enterprise comes across a stranded civilian ship, the Kobayashi Maru, which happens to be perilously disabled inside a Federation-Klingon neutral zone. If no rescue is attempted, the ship's passengers will die. But if the starship enters the neutral zone, it will be a violation of a peace treaty and be considered as an act of provocation toward the Klingon warships that just happen to appear and blow both other ships to smithereens. It's a classic no-win."

Beckman sighed loudly and slumped back in her chair, beginning to lose interest. Clearly, she thought, the Intersect had fried the poor boy's head.

Chuck sighed back at her, somewhat defiantly. He was definitely leading somewhere. "Anyway," he over-enunciated, "What makes this particular test so special is that nobody had ever successfully managed to rescue the Maru without sacrificing the Enterprise. That is, nobody except one James Tiberius Kirk."

The lanky nerd paused, rocking slightly back and forth on the balls of his feet. He was waiting for someone to bite and ask the obvious. He allowed his mouth to curve slightly into a grin, and glanced over to Sarah. She smiled back, guessing as to how Chuck was going to talk his way out of his predicament. She knew the answer to the implied question - _Khan_ was one of his recent picks for Bartowski Movie Night.

The General finally relented. "Okay, Chuck. Tell us. How did Captain Kirk win the simulation?"

Chuck returned his attention to the screen. "I thought you'd never ask. Kirk, who wasn't yet a captain at the time, mind you, beat the simulation by cheating. Well, not technically cheating. He changed the rules of the game to his advantage by reprogramming it so that he would be able to convince the Klingons to help him rescue the civilians. He was commended for his 'original thinking.' He defended his actions by saying that he never believed in no-win situations."

Chuck was pleased with his roundabout analogy. His confidence regained, he stood up a little straighter and spoke openly and honestly. "You see General, we're facing our own Kobayashi Maru moment. The Intersect is destroyed, again, except for me and what's in my head. Scenario Seven proved to be a miserable failure. Castle is compromised. Our covers are blown. The safe thing for you to do is lock me away in a bunker. But that's not boldly going to where any, um, joint NSA-CIA intelligence initiative has gone before. We can work this to our advantage by changing the rules of the game. We can take down this Ring group if we play our cards right."

Now the General was interested. Maybe the Intersect program could be salvaged, despite everything. She leaned in again. "Go on."

Casey stepped forward before Chuck could elaborate. "I'm sorry ma'am, if I may interrupt before too far. What exactly is Scenario Seven?"

Beckman nodded to Chuck, allowing him to recite what the Intersect had brought to the forefront of his conscience a few minutes earlier.

"Shortly after Bryce sent me that email almost two years ago, the NSA and CIA regrouped to cover their collective asses. Project Omaha was officially disbanded and the hairier parts were rolled into a new program – Project Plato. Since my continued existence proved that a human mind was capable of processing encoded steganographic images, an upgraded version of the Intersect was to be developed that would push the limits even further. In addition to mundane and boring stuff like the entire freaking dossier of American espionage, the NSA and CIA saw opportunity to build an army of mega-knowledgeable superspies. Think of it as instant on-demand learning. If a mission called for any of tens of thousands of specialized abilities, the Intersect could retrieve and force a flash for all pertinent information. A single agent could be an expert scholar of Renaissance-era basketweaving on Monday, a fully capable jumbojet pilot on Tuesday, a brain surgeon on Wednesday, an astrophysicist on Thursday, and a world-class Nordic skier on Friday. Full fluency in every known language was possible. Really amazing stuff." Chuck looked at the General, his eyes darkened. "All built on top of my father's stolen technology."

Chuck paused to catch his breath, truly realizing for the first time the extent of power he now held inside of him. _Holy crap_, he thought to himself, _no wonder Bryce warned me about this and my dad had spent years as a recluse to stay as far away from it as he could. It is entirely too powerful to allow into the wrong hands, even if those hands belong to the good guys. This is as close to absolute power as one can get. And absolute power corrupts absolutely. I must be cautious. And mindful of my own impulses. This is heavy.  
_

Sarah interrupted Chuck's reverie, eyes pleading for him to continue. She had to know what the man she loved had willingly got himself into. "So that explains Plato, but what about Scenario Seven?"

"Once the scientists got the brain-mapping and the basic theoretical mechanics of uploading this new type of data figured out, suitable agents had to be found. Students at Stanford, MIT, Cal-Berkeley, and Harvard were surreptitiously tested much like I was for pattern-recognition and cognitive potential. The results were much less than what was hoped for. The highest scoring candidates only retained one-third of what I've been able to grasp. I don't know why my brain functions differently, but that's just how it came down. Despite these results, the top tier of about 75 candidates was recruited and groomed to undergo a series of psychological and physiological evaluations and scenarios."

"The first few tests rooted out those who wouldn't be able to emotionally handle the stresses of the role. The next few scenarios focused on the Intersect itself. After the fourth round, the 20 or so remaining candidates were loaded with the basic Intersect framework and a teeny-tiny fraction of a percent of dummy data was uploaded and tests were conducted for basic retrieval. No cross-referencing, no data-branching, just simple 'tell me what you see' tests. Two candidates didn't survive, and another will live out her days in a padded room. The fifth and sixth rounds upped the ante a bit by beginning to extrapolate semantic meaning from related images. By the time it came to begin tests for the seventh scenario, Project Plato was down to 8 lucky surviving finalists."

"Scenario Seven was the first test that moved into the realm of applied on-demand ability absorption. It was determined that the quote-unquote easiest topic to begin with was an elementary-level handling of the Afrikaans language, since it shares many lingual characteristics with American English."

Chuck paused, and choked back a bit of emotion. "All eight fared no better than the Fulcrum agents at Meadow Branch."

John Casey growled at the General's video screen. Sacrificing one's self for the greater good of your country was one thing, but being subjected to experimental human testing, that was doomed to fail from the start, was another. That crossed even his blurry ethical line.

Sarah brought her hand up to her mouth, and tears welled up in her eyes. "Oh my God. That is horrible." She couldn't help but to think about those poor students, and how they were lured into cooperation much like she had been - with false promises playing up the fairytale James Bond life, excitement, travel, and intrigue. Those students should've been scientists and engineers, but instead they were used as guinea pigs and their bodies were sent home to their parents with cover lies of auto accidents and suicides and the ever-convenient mugging. The only thing these unsuspecting souls ever did wrong was to have the misfortune of being in the wrong place at the wrong time.

She had never been completely ashamed of her employer and her charge until now. Until she met Chuck, she'd always believed that the ends justified the means. He'd changed her and she'd seen her perception of herself as an agent and as a person flip. This revelation of Project Plato shook her core belief system. Her mind played back the various missions through the years – all the assassinations, seductions, lies, charades that she and Bryce…

"General?" Sarah spoke up. "If Project Plato was a total failure, why was Bryce going to be Intersected? Wouldn't he fare the same as those candidates? Wouldn't he have ended up dead anyway?"

General Beckman had figured this question would come, and didn't look forward to answering it. "Perhaps. But it was his choice. He volunteered. He was tested years ago at Stanford, prior to his joining the agency. His retention capabilities weren't in the same league as Chuck's, but they were just as high as anyone tested for Plato. We believed that his years of CIA training and his exposure to the Intersect project, particularly seeing it firsthand and knowing that it was a reality, would allow his mind's defenses to be more accepting. Our research team placed above-even odds at him surviving a full download. He was willing to take that bet. And, given the circumstances, so were we."

"That egotistical little prick couldn't stand that Wonderboy could outdo him." Casey muttered under his breath. His comments were within earshot of Chuck and Sarah, who both smiled in spite of themselves.

He was also apparently within earshot of the General. "What was that, Colonel?"

"Um, nothing ma'am. What now? How do we move forward?"

Beckman's focus returned to Chuck. "I was hoping Mister Bartowski had a plan of action. That's what this little detour has been leading toward, has it not? You were about to tell us why I should keep you above ground and how your reacquisition of the Intersect will help us defeat what remains of Fulcrum and take down this mysterious Ring?"

Chuck exhaled and tugged at the bottom of his untucked shirt in an effort to appear less like an expendable asset. He knew his whole future depended on this recommendation. The next few minutes would determine if he'd ever see his friends and family again, if he'd ever have a chance at a future with Sarah, if he'd ever have a chance to make something of himself. It was now or never. He was ready.

"General," he began, demonstrating an amount of confidence that surprised even himself. This wasn't the Intersect taking over, this was Charles Irving Bartowski manning up and taking charge of his life. "This is how I see it. Much like Kirk's circumvention of the rules of the Kobayashi Maru simulation, we an opportunity to rewrite the rules as they currently exist."

"Fulcrum only knows for certain things that they'd personally observed. Every other thing they think they know comes to them from moles that are inside the NSA, CIA, and elsewhere. I say we use what they think they know against them. They believe that I, as of a few days ago, was the Intersect. They know my father designed it. But they also know that their mass download at Black Rock was a failure and blame that on my father purposefully introducing a flaw. They surely know by now that I was issued a pay packet, and that Casey and Sarah were reassigned. Naturally, they'll come to the logical conclusion that the Intersect was removed. Jump ahead to today. Word soon will get to them and to The Ring, if it hasn't already, that the Intersect was destroyed. The beauty part is that nobody saw that I uploaded the new Intersect. The only ones who know of my kung fu hustle are either present right here right now, dead, or indefinitely detained. Is everybody with me so far?"

"So you are saying, Chuck, that we should let them think that the Intersect is completely destroyed?" Beckman nodded. "I like it, but that doesn't explain why I shouldn't put you in a bunker for your own good."

"You shouldn't put me in a bunker because I'm safer out here. Security through obscurity. If I suddenly disappear, and their cells start getting picked off one by one, they'll know I still have it in my head, and they'll come after me. And frankly, given that we aren't certain how deeply they've infiltrated, I'm better off here being Carmichael." Chuck could see that the General was considering his argument, so he quickly added. "Plus, now that I can go zero-to-awesome in 2 seconds flat, my talents would be wasted underground. I'm better off in the field."

The realization hit him as soon as the words left his mouth: he had just volunteered to be a full-fledged agent. The admission wasn't lost on anyone else either. Casey grunted approvingly. Sarah was in shock. Beckman wasn't entirely convinced.

"You want to be Carmichael, Chuck? Did I hear you correctly? You wish to become an agent?"

"Yes, General, you did, and I do. When I was in that room with Bryce, I had an epiphany of sorts. Everything in my life was leading me to this. Stanford, my dad, that email on my birthday, working with Sarah and Casey. For some cosmic reason, I'm meant to be the Intersect. Of everybody who was given those exams and recruited, I am the only one who can do what I do. This is how my life is supposed to be. I know I whined about wanting to be normal and getting the Intersect taken out, but that's because I saw it as something that was pushed onto me without my consent. But when it was finally removed, I felt empty. I looked back at all the lives I've directly and indirectly saved, and all the good the team has done, and I realized that I'm not normal, and I never will be, and that my purpose is to serve the greater good. When I look at my sister, her new husband, and my friends, I see them as examples of the people who need to be protected from the likes of Fulcrum and The Ring. I don't trust anyone more to do that for them than me. So, when I was standing there in front of that Mac terminal, I am absolutely certain I made the right decision. I am meant to be the Intersect."

The very act of verbalizing what he had been thinking came as an immense relief to Chuck. As the words flowed out of his mouth, color came into skin and vibrancy flooded his eyes. He had said his piece and was willing to accept whatever judgment came his way.

The General soaked in the scene that had played out in front of her. Admittedly, the confident and assured Chuck Bartowski standing here today was leaps and bounds more impressive than the meek and bumbling Chuck Bartowski who first seemed lost in a strange new world many months, or even weeks, ago. And he had that damn sincere charm about him.

"Colonel Casey, what are your thoughts on this matter? If given proper training, do you believe that Chuck can become a capable agent?"

The NSA agent looked at Chuck, gave a small nod, grunted, and allowed a smile. John Casey actually smiled, but only for a second, before he answered in the affirmative. "Yes, General, I do. I would be honored to be on his team."

General Beckman turned and addressed Sarah. "Agent Walker? I'll go ahead and assume you feel the same way?"

Sarah couldn't be any more proud of Chuck than she was right now. Even if it threw a wrench in their pursuit of a relationship together, she was glad Chuck had accepted and embraced that he was special and heroic and most definitely extraordinary. She looked across the room and lost herself in his brilliant brown eyes for a moment, before addressing the video screen. "I absolutely agree."

General Beckman nodded in acknowledgement of Casey and Sarah's input and paused for dramatic effect. It wasn't too often in her line of work where she got to deliver good news. "Very well, then. Congratulations, Agent Carmichael. You've convinced me that there may still be some potential for you yet."

Chuck stood up straight, mimicking Casey and Sarah's stances. "Thank you, General. I will not let you or my country down."

"I'm glad to hear it. I will make the necessary arrangements and we will go through the formalities in a few days. First order of business, however, is to establish new covers and a new base location. Sarah, I'm sure you'll be heartbroken to have to stop serving frozen yogurt. Work it out amongst yourselves and give me a recommendation in no later than 24 hours." She reached forward to press the disconnect button, but hesitated for a moment before disconnecting. "Welcome aboard, Chuck."

When the screen went dark, Sarah rushed to Chuck and nearly knocked him over with affection. "I'm so proud of you!" she said between joyful kisses. "You'll do great!"

"Oh jeez, don't start this already." Casey groused playfully.

Chuck flailed his arms as Sarah ignored her partner's comment. "Sar.. Sarah? Could… could you do me a favor and not squeeze me to death? The adrenaline is wearing off and, to be quite honest, you are hurting me. Remember? Kung fu? Hi-ya. Pulled… everything?"

"Oh! Right. I'm so sorry." Sarah jumped back. "We should, um, probably get back and see if the reception has wound down yet. I'm sure Ellie noticed our disappearance."

Thirty minutes later, one happy couple walked up to Casa Bartowski to find that the other happy couple was still in the courtyard, saying their goodbyes to the Awesomes. They were the last remaining guests to go home.

Devon was the first to spot them. "Hey Chuckster, I saw that you two kids snuck out for some alone time. Nothing wrong with being in the celebratory spirit, am I right?" He nodded, alluding to the obvious. "That is awesome."

By that time, the newly minted Dr. Eleanor Faye Woodcombe was beside her new husband and promptly smacked him on the arm. "Hey little brother, I just wanted to thank you again for saving the day. You're my hero." She leaned in for a hug. Chuck gladly accepted, hiding the inevitable wince of pain.

"Anything for my big sis."

Ellie moved on to hug Sarah, but kept talking, as she was apt to do. "Don't worry about us. We'll be out of your hair shortly. We just wanted to clean up the courtyard a little bit before heading off to the Airport Hilton. Our flight leaves pretty early, and we'll be gone for 10 days."

"Oh Ellie, don't worry about it." Sarah responded genuinely. "You too get out of here, begin your new life together. Your honeymoon awaits. Go. Shoo. Have fun. We'll take care of things here."

Ellie released, smiling and on the verge of happy tears. "You two are the best. I don't know what we would've done without you." Minutes later, the newlyweds were on their way, leaving Chuck and Sarah to bag up the various balloons and streamers and empty bottles of champagne.

Casey joined them a few minutes later when the coast was clear, and waited for a private moment with Chuck as they were carrying trash bags to the curb. "You did good today, Bartowski. I meant what I said in the Castle."

"Thank you, John, that means a lot."

Casey grunted and grinned deviously. "Don't screw it up, moron." He paused for a moment and nodded in the general direction from which they came. "Now go back there and sweep Walker off her feet. You two have been dancing around each other for nearly two years. It's sickening, really." He pulled out a cigar and slapped Chuck on his back and retired to his apartment. "Good night, Chuckles."

Chuck walked gingerly back toward his own residence and found Sarah waiting for him by the fountain. He grabbed her hands and kissed her gently. "Shall we go inside?" he asked, already leading the way.

Inside, on the kitchen's bar counter was a single bottle of champagne and a note. "C & S, thanks again for everything. You two are awesome! -Devon." Chuck picked up the bottle, looked at Sarah suggestively and gave her the ol' Bartowski Eyebrow Dance.

As the door to Chuck's room closed and locked behind them, Sarah spoke loudly to the bugs she knew were placed in hidden locations. "No need for audio coverage Casey, I'll handle surveillance tonight."

She and Chuck both laughed when they heard Casey's voice yell from the next apartment over, "Roger that!"


	3. Preparation

**Chuck vs The New Intersect**

**Chapter 3**

The light streaming through the window of the front bedroom of Casa Bartowski was causing the room's two occupants to stir. The beautiful blonde agent woke, sleepily opening her eyes. Once able to gain her bearings, she looked up at the man beside her in bed and smiled contently. _I could get used to thi_s, she thought as she recalled the events of the previous night_._ _I could certainly do this every day. _She leaned in closer to her lover and nuzzled him gently on his neck.

Chuck, eyes still closed, giggled softly at her touch, betraying that he was only pretending to still be asleep. Sarah's head perked up, and she kissed him on the tip of his nose. He involuntarily scrunched at the sensation.

"You're awake," she teased.

"No I'm not," he whispered back. "I'm asleep. Shh."

"Fibber."

"Nuh uh. Shh." He smiled and he peeked one eye open, only to find her staring back at him. He immediately squeezed it shut and whispered. "Sleeping."

"Mmm hmm. How long have you been awake?"

"I'm not awake. Sleeping, remember?"

Sarah sighed, amused, and laid her head back on his shoulder. "OK, well, why are you still sleeping?"

"Because I don't want to wake up and have this only be a dream." Chuck answered honestly, with a hint of fear and uncertainty in his voice. He had been waiting two years for the chance to wake up next to Sarah for something other than a cover. He was pretty sure everything had happened as he remembered it, but he wasn't willing to take any chances. If it was really a dream, he wanted to hold onto it for as long as he could.

Sarah propped herself up on her forearms, and playfully bumped his shoulder. "Chuck, I assure you that this is real."

"Promise?"

"Promise."

He grinned at her and the playfulness returned to his eyes. His mouth moved into a Cheshire smile. "Prove it."

Showing her trained dexterity, she rolled on top of him into a straddle position and kissed him deeply. Before coming back up for air, she nibbled at his bottom lip. Leaning back, she smirked. "Was that real enough for you?"

Chuck was wide awake now, lying underneath her with his mouth slightly agape. He was unable to speak, but nodded in the affirmative. After a few moments, he regained his sense. "Sarah? I'm stiff."

She wiggled a bit and grinded her hips down onto him. "I can see that."

"No," he grimaced. "Well yes. But that's not what I meant. I'm stiff from my injuries. I don't think I can move. My muscles and joints tightened up overnight."

Sarah hopped off of him in one swift motion. Clearly flustered, she fawned over him, and then bolted out toward the kitchen. "Chuck, I'm so sorry. I thought you were… I just… I'm so sorry. Let me go grab you some painkillers."

When she returned with water and a few small white pills, Chuck gratefully accepted her offering. "Don't be embarrassed. You know I would if I could. Again, for the fourth time." He sighed wistfully, "You have no idea how much I would. Last night was incredible. It was perfect. You were perfect."

She blushed, but her mind was racing for a way to salvage the situation in a mutually satisfying way. "Maybe a hot, steamy, shower would make…" She paused briefly to raise her brow suggestively. "… us… feel better?"

About 90 minutes later, the couple emerged, dressed casually, from Chuck's bedroom. She was wearing a pair of jeans and a tanktop that she'd stashed there several weeks earlier in an overnight bag and he was dressed in loose cargo shorts and a Stanford t-shirt. He was still shuffling about at three-fourths speed, but he was clearly feeling better than he had earlier.

The lingered in the kitchen, rummaging in search of things to make for breakfast only to find the normally well-stocked fridge and pantry now bare. Ellie had apparently banked on her baby brother surviving on takeout and junk food while she and Devon were on their honeymoon.

Chuck was trying to figure out what he could possible concoct from a package of string cheese, half a bottle of orange juice, some of Awesome's protein powder, and a box of baking soda when his and Sarah's iPhones simultaneous chirped in indication of a text message.

They both looked at their respective displays and groaned. It was Casey, inquiring "You two decent? We have work to do." Chuck texted back "Yes. Come on over. Bring food."

A few seconds after hitting the Send button, Casey walked through the front door carrying a carton of eggs, some peppers, and a tomato. He unloaded the food on the counter and helped himself to the stool at the bar. "I brought it. You cook it." He smirked and gestured dismissively. "Go on. Chop chop."

It didn't take the Intersect for Chuck to figure out that the only real option for the given ingredients was omelets, so he got to work. Luckily, it was one of the few things that he already knew how to cook well. Plus, he was buoyed this morning by the assistance of a lovely sous chef with considerable knife skills already dicing peppers.

"So Casey," he began as he cracked the eggs into a mixing bowl, "what now? What are our options? Where do we go from here?"

The gruff man responded, "Your nut ball antics with Beckman were enough to keep you out of a bunker for now. She liked the idea you pulled out of your ass last night, now we just have to figure out the logistics of how to pull it off. We need to determine our new covers jobs. We have to find a new base of operations. We need to come up with a story to throw the hounds off our scent."

"We have to establish new living arrangements," Sarah interrupted, smiling at Chuck. She sauntered over to him, tilted her head and batted her eyebrows melodramatically. She pawed his arm sweetly and spoke softly and innocently, for effect. "The hotel already thinks I'm moving out. You wouldn't leave little ol' me homeless and out on the street, would you?" Her demeanor suddenly turned lusty, and the grip on his arm tightened. "Besides," she purred, "I could make it worth your while."

Chuck tensed and his eyes bulged as he processed that she was hinting at wanting to move in together. She interpreted his shock as a negative reaction and retreated. "I could always re-up at the hotel or get my own apartment if it's too much too quick for you for you or if you'd just rather not…"

Chuck interrupted her rambling by pushing a finger on her lips. "Nothing would make me happier than getting a place with you. We've danced around our thing-under-the-undercover-thing for nearly two years. I'm not doing it anymore." He leaned down and kissed her. "This is for real."

Casey groaned and cleared his throat loudly. "If you two are gonna be like this all the time, I'm going to gouge my eyes and ears out."

Without breaking their embrace, Sarah grabbed a dishrag off the counter and hurled it across the kitchen, hitting Casey in the forehead, eliciting a grunt and a reluctantly mumbled "Nice shot, Walker."

Chuck plated their breakfasts, and the trio moved to the table. "I have a basic idea of what we can do, but I need to make a call first." He grabbed his iPhone and started scrolling through his contacts list as he kept talking, "It's really just a variation of my grand Charles Carmichael plan. There are still some rough edges to smooth out, though." Finding the contact he was looking for, he pressed the dial button and held the phone up to his ear. "I don't necessarily see the America's Cup in my future, but who knows? Maybe there's still time." He shrugged, then spoke into the phone. "Hey Dad, it's me. Want to come over for some breakfast? We need to have a chat."

Sarah and Casey looked at each other from across the table and communicated silently. Orion wasn't part of their assignment, but they both knew that keeping tabs on him and gaining his cooperation would be a huge advantage in their fight against Fulcrum's remnants and The Ring, not to mention in keeping General Beckman off their backs. Plus, equally if not more importantly, he was Chuck and Ellie's father. They would both do everything in their power to keep his family – a group they now are considered part of - together.

A few minutes later, a black Suburban SUV pulled up outside. Stephen Bartowski hopped out of the backseat and his three NSA bodyguards took up perimeter patrol around the residence. Inside, he greeted his son with a hug, Casey with a handshake, and Sarah with a peck on the cheek. Cutting right to the chase, he quipped, "So, what's the occasion?"

"Well, Dad. You see, here's the thing." Chuck began, stammering due to nervousness. After everything that the government had done to the both of them, and the months-long effort and coordination it took to remove the Intersect from his head, he wasn't sure how to explain that he voluntarily downloaded the Intersect again. He didn't have to continue.

"I already know, Charles. You downloaded it again."

"How do you…"

"I'm Orion. I know these things. I have my methods of keeping tabs on you."

"So you're not…"

"Mad? I'm certainly not thrilled that you are going to stay involved into this world. But that's the protective father speaking. I worry about you. I'm allowed." He sighed before continuing. "But as Orion, as the Intersect's creator, I can't deny that you have some kind of destiny with that thing. It's like it was built just for you. I have no doubt you'll do a lot of good as long as you keep your wits about you and don't let the agencies control you to the point where you lose what makes you you."

Chuck smiled and his expression visibly relaxed. "Great. I know that with Sarah and Casey and you around to keep eyes on me, I'll be fine."

Stephen looked down, purposefully avoiding contact. "Son, I can't stay."

Chuck's smile vanished. "Wh... Why not?"

"It's too dangerous. Our identities have been compromised. They know who I am and what I've done, and they know who you and your sister are. It's better if I disappear, fore your sakes. I can slip away from the suits outside and go back in hiding. It's safer. We make too tempting of a target together if I stay around. You're in good hands here."

A thousand emotions swirled inside Chuck: confusion, desperation, hurt, sorrow. Anger won out. "You can't leave. You promised Ellie you would stay. You promised me you would stay." He began to yell. "You owe it to us. You already left us once to fend for ourselves. I know now why you did it, but that doesn't make it hurt any less if you just go out and do it again. I can handle it, Dad, but it'll kill her. You have no idea how happy she was and how much it meant to her to have you back for her wedding. I won't allow you to do that to her again!"

Stephen spoke softly, still avoiding eye contact. "I'm sorry, son, but I have to. I have no choice."

"Yes you do! I can fix this!" The intensity of his son's suddenly authoritative voice made Stephen finally look up. He remained silent and allowed Chuck to continue. "I've worked this out. I can keep us all together." Chuck took a deep breath to renew his calm. "There's only one catch. You have to work with us. You, Dad, are our new cover."

Tension was thick as the four adults stood in Ellie's dining room. Seconds felt like minutes, and nobody said anything as Stephen debated internally whether or not Orion should rejoin the government ranks after several years as one of the most wanted men in the intelligence arena.

Finally, he walked to the nearest chair and sat down. "Alright, Charles, what's your plan?"

The two agents exhaled and joined him at the table. Casey muttered mostly to himself, "The nerd's idea had better be brilliant or we're screwed."

"We work together, as father and son, and try to figure out what's going on in my head and how to improve it and keep it running. If I'm going to be running around being a superspy, I need to understand it and learn to control it. Surely Beckman can see that it is in everyone's best interests for the only guy to can absorb this thing to not accidentally turn himself into a vegetable. I want you by my side, Dad." Chuck managed a crooked half-smile, looking like a puppy seeking its owner's approval.

Chuck began to nervously pace. "The gist of my plan is that we hide in plain sight. Since our covers are already blown in the spy community, we don't even try to hide it. In fact, we ought to play it up. We see to it that the leaks and informants within the agencies get fed the story that whatever you did, Dad, at Black Rock permanently fried by brain circuitry so bad that the Intersect can't be reinserted. We leak the results of Project Plato. We let them think that the Intersect died with Bryce. Hell, I'd go so far as to arrange a Congressional investigation Bourne-style to further emphasize that the Human Intersect Project is dead and written off."

Casey grunted approvingly and nodded. "Go on."

"So that leaves us with needing to explain to the spook-world why we're still out here together as a team." Chuck stopped and looked at his father. "The four of us." He paused a few more seconds, then continued. "We make it look like I've been recruited based on my prior exceptional untrained field performance and that Orion and I are working on a new project completely unrelated to the Intersect, and that you two," gesturing at Sarah and Casey, "are our muscle. Instead of watching one of me, you guys are now tasked with watching the two of us."

"OK, Chuck," Sarah questioned, "so what's the public cover? What do we tell the outside world?"

"I'm thinking it's about time the Bartowski family gets a little recognition and compensation, courtesy of one Ted Roark." Chuck grinned his megawatt smile. "It would be ideal if his soon-to-be-named replacement at Roark Industries were to discover in a legal audit that the dear company founder based some crucial work off of various designs he stole from his old college pal Stephen J. Bartowski without paying for them or giving proper credit. And not wanting to risk any unflattering public attention, he'd see to it that the issue was quietly taken care of with a nice hefty research and development contract. I'm thinking twenty mil might be enough to get us off the ground. That sounds like a good round number."

Casey did a spit-take, sending orange juice spraying across the table. "Did you say twenty million dollars?"

Chuck rocked forward on the balls of his feet, his smile growing bigger. "Yep. I figure Roark owed Dad at least that much. It's not taxpayer money, calm down. Anyway, we take this money and found a business that has the public cover of doing next-generation graphics processing hardware acceleration research. Well, Dad would be handling that part. I would be…"

Sarah interrupted him. Her own smile growing, she completed his thought. "Designing the next generation of video games, just like you always wanted to do. I think it's brilliant!"

"I think so, too" came the opinion of the elder Bartowski. "I'm in. This might just work."

He and Sarah stood up and hugs were given all around. Only Casey remained seated. "Hold up one second. Neither Walker nor I know squat about designing video games. What are we supposed to do?"

Chuck paused. "I haven't figured that out yet. I was thinking we could hire Sarah as an office manager or marketing director. Not sure about you, though, Cas. Maybe we can sell Beastmasters on the side?" That evoked a growl from the NSA agent. "Maybe we'll just play that one by ear. We'll figure something out."

Sarah put her arms around her boyfriend's waist. "I could do marketing or sales or whatever you need me to do." She then squeezed playfully and added, "As long as you don't expect to prance around as a booth babe." The brief thought of Sarah in a skimpy outfit made Chuck blush and zone out, but he was brought back to reality by her next question. "Have you given any thought to a company name?"

"I'm not sure about that either. I'm tempted to honor some of my geek roots in some way, taking a pop reference and tweaking it. Maybe FusionTech based on the Mr. Fusion power source on the Delorean in 'Back To The Future.' Or, how about ForceThree as a take-off of the Triforce in the Zelda series. Or, like, the company MacGuyver worked for was the Phoenix Foundation, so I'd twist that into something like Fenix Systems spelled 'F-E-N-I-X.' "

Casey groaned. "If I ever have to work at a place spelled that dumb, I swear I will not hesitate to K-I-L-L-Y-O-U. Why don't you stick to the basics like Nerds-R-Us or Dweebs-N-Things or Moron, Inc.?"

Sarah looked at him dully and chose not to acknowledge her partner's ever-helpful insights. "What about that show that one was on when we were kids? It had the guy from Battlestar in it?"

Chuck looked at her quizzically. "Miami Vice?"

"Huh? No. Not that one. The one where the guy jumped into people's bodies every week. It was the one show my dad would regularly watch every week. He always compared it to us moving around so often and changing our names and identities and backstories." Sarah was getting frustrated. "It was 'Jump' something. Or 'Hop' maybe. I had a crush on the lead actor guy. Ugh, it's on the tip of my tongue!"

Stephen stepped forward. "You mean 'Quantum Leap' with Scott Bakula? That was a damned good show for its time."

"Yes! That's it! How about naming the company 'Quantum' something?"

"Ooh! I got it. We'll call it QuantumFX, or QFX for short." Chuck beamed, pleased with Sarah's suggestion. "I like that. Unless there are any objections, I say we go with that."

Casey groaned again, "Oh boy." For some reason, Stephen looked at him and chuckled.

* * *

A few hours later, the group was in front of the main video screen in the Castle, with Chuck explaining their plan to General Beckman. After he went over the big picture concepts and basic logistical needs of their plan, she leaned forward toward them to give her verdict.

"I must say that you leave me in a quite an interesting predicament. Your proposal is as good as any that our strategists could come up with, as unorthodox as it may be, but leaving you and your father out in the relative open is a risk." She furrowed her brow and internally debated the pros and cons of the situation. "However, that may play out to our advantage. I'm going to give you the go-ahead. We'll dub this mission Operation Canton."

The team breathed a collective sigh of relief. Sarah bit the inside of her lip to force herself not to be overcome with emotion. Chuck – her Chuck – was not only going to stay out of a bunker, he was given the OK and financial backing to start pursuing his dream, and she was going to be there by his side. She snuck a glance over to him and found him doing the same back to her.

Beckman continued speaking and the two snapped back to attention. "Obviously, it will take a few weeks to get things setup and in place. In consideration of this and Chuck's need to recuperate from his injuries, I'm ordering you four to keep activity to a minimum until then. Your only objective is to scout for a suitable secure office location and new apartments and prepare for transition out of Castle. Consider it a vacation, it will likely be the only one you get for a long time."

The General visibly softened. "The final order of business is to process the formal paperwork for the Misters Bartowski." The video screen's display shuffled around to show employment terms, various NDAs, and other fine print legalese. "A retina scan will serve as your signature to make things official." The father and son stepped forward and both pressed the needed buttons at the console to illuminate their respective right eyes in green light. Beckman nodded, "Congratulations, Agent Carmichael and Agent Orion. I'd like to be the first to extend welcome into the National Security Agency."

* * *

The next afternoon, Sarah and Chuck were lounging at Casa Bartowski, sprawled across the living room couch, searching for their future home. She was going through the classifieds in the local newspaper and he was on his laptop browsing online.

Their iPhones simultaneously chirped again with a text message from Casey telling them to turn on CNBC. Chuck shrugged and reached for the remote, but it was slightly out of reach. Instead of getting up to grab it, he whined playfully to Sarah. "Saaaarah, I can't reeeeach it. Can you get it, I'm innnnjured." She rolled her eyes at him and stuck her tongue out as she pushed herself up to retrieve it.

She clicked on the TV in time for the anchor to announce, "Roark Industries founder and CEO Ted Roark was found shot dead in his Malibu home, authorities are reporting. Police have no suspects at the moment, but believe he was the victim of a botched robbery attempt. Chief Operating Officer Benjamin E. Gesserit has been named interim CEO."

Sarah was about turn the TV off again when the anchor moved on to the next story. "Buy More Incorporated announced quarterly earnings today, falling well short of analyst's expectations. Operating revenues were down 53% year-over-year. It is expected that the Southern California retail chain will undergo massive employee restructuring and the closing of lowest-performing stores."

Chuck and Sarah looked at each other, jaws dropped, before Chuck spoke up. "I've got a bad feeling about this."


End file.
